DISCLAIMER You are free to use the processed and annotated TCR:pMHC tables in this repo for your research. However, the authors request priority in publishing a meta-analysis of the dataset aggregated and stored here. This message will be removed once this study is officially published. Thank you for understanding.
This repository contains a set of scripts that automate downloading, pre-processing and annotation of TCR:pMHC structural data with the following functionality:
scripts in annotation/src/
folder
scripts in structure/src/
folder
To run the pipeline execute the run.sh
script. It will proceed with the list of PDB ids from result/extended_pdb_ids.txt
. Some parts of the script are rather time-consuming, especially structural data annotation (downloading PDB files and running GROMACS). The results will be stored in result/
folder:
final.annotations.txt
contains the list of PDB entries that passed filtering and their annotationstructure.txt
or structure.txt.gz
contains annotated data on the amino acid level, with pairwise residue distances and interaction energies for TCR:antigen pairs.structure.mhc.txt
or structure.mhc.txt.gz
contains annotated data on the amino acid level, with pairwise residue distances and interaction energies for TCR:MHC pairs.Meta-analysis of the resulting dataset is stored in the analysis/
folder.
The pipeline is written in Groovy and Python (written in 3.5
but should run under 2.7
) and requires both to run.
Three third-party software tools that are required:
pandas
and BioPython
(for both condas) packages.openmm
and pdbfixer
, available only in Anaconda.blastp
and makeblastdb
are in your $PATH
. We highly recommend you to use homebrew
for OSX / Linux for BLAST and IgBLAST installations.1.4.0
version. Ensure that igblastp
is in your $PATH
.gmx
is in your $PATH
.